>input_sequence_68343
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--------------------------------------------------------ATGGCGAGCCACGGGCATGAGCAC
GGCCTGCTGCTCGACCCGGCCGCGCTGGCCTACTCCTGGGCCGCCGAGCCGGAGTTCCCGCCGCAGCTGCTCGCCGCGCT
GGGGGAGTACCTCTCCTCCTCCGCCGCCGCCGCCGGCGCCTCCCACGGGGACCATCAGTCTGCCGTCGATACCGACGCGG
ACGCGGAGGCGGACGACGAGTTCATGATGTACGAGTTCAAGGTGCGGCGGTGCGCGCGCGCGCGGAGCCACGACTGGACG
GCCTGCCCCTACGCGCACCCGGGGGAGGCGGCGCGGCGCCGGGACCCGCGCCGCGTGGCCTACGCGGGGGAGCCCTGCCC
GGACTTCCGCCGCCGCCCGGGCGCCGCGTGCCCGCGGGGGTCCTCCTGCCCGTTCGCGCACGGCACCTTCGAGCTCTGGC
TCCACCCGTCCCGCTACCGCACCCGCCCCTGCCGCGCCGGCCCGGCCTGCCGCCGCCGCGTCTGCTTCTTCGCGCACGCG
GCCGGGGAGCTCCGCCTCGCCTCCCACCACAAGGGGCCGGGGCCGGACTCGCCGCCGGCGCTGTCGCCCAAGTCCACGCT
GACGGCGCTCTGGGAGTCGCCCCCGGTGTCGCCCGTGGAGGGCAGGATGAGGTGGCTGGACGCCATAGACGACGCCGCCG
CCGCCGACGCCGAGGTCGGGGAGATCATGCTCGCAATGCAGCAGCTCAGCTTCGCCAACGCAGCA------------CCG
TCAGGAACGCTGCCGGCGGTGACGGAGGACGACGGGCCGGACCTGGGGTGGGTGTCGGAGCTGGTCATGTGA--------
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>chr1A_1_TraesCS1A01G346500
CTGAGGCTTTTTAACACATGACACTATTCCTCCTCCCGGACCAGGAATTTGTCTTTTTTGTACAGGTCACATTTCAACGT
TTTTCATTCTGAAATTTTACACACATAGGCATAACATACTTGTTTACTTGCACAATTTTTTCAGATTTTTTTGAAACCGA
AAAGTTTGAATTTTGATTTGTTTTCAAAAAAAGGCCTCCATGGCTCCCGGGAGCCAAACGTCCGTTCTCTATGTCTAGAA
TCCAGAAGAGGAAGAAAAATAAAGGCGGGCGGGGTGCGTGCGTGCGTGCCGGCGGCGGAGGAG------------AGAAA
CCATCCCGGCCGCGACGTGGCGGGCAACATGCAGCACCCGCCTCGACGGCGCTCCACGTACCCTCGCCCACCCCCACGTA
CCCCGCCCCGCGCCAAAACCACCCCACGCCGATAGCCCCCCGCCCGCAACCAACAGCGGTCCATGCGATACCGCCCCTCC
CCGCACCGGCGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTCCCCCACACCACCA--CCACCACCACCGCCGCCGGTTACCGTCACGGCG
TGTCATCACACCTCTCTCTTT--CCCTCTCCCCCTCTGACAAGGACAAGGACGGCCATGGCGAGCCACGGGCATGAGCAC
GGCCTGCTGCTCGACCCGGCCGCGCTGGCCTACTCCTGGGCCGCCGAGCCGGAGTTCCCGCCGCAGCTGCTCGCCGCGCT
GGGGGAGTACCTCTCCTCCTCCGCCGCCGCCGCCGGCGCCTCCCACGGGGACCATCAGTCTGCCGTCGATACCGACGCGG
ACGCGGAGGCGGACGACGAGTTCATGATGTACGAGTTCAAGGTGCGGCGGTGCGCGCGCGCGCGGAGCCACGACTGGACG
GCCTGCCCCTACGCGCACCCGGGGGAGGCGGCGCGGCGCCGGGACCCGCGCCGCGTGGCCTACGCGGGGGAGCCCTGCCC
GGACTTCCGCCGCCGCCCGGGCGCCGCGTGCCCGCGGGGGTCCTCCTGCCCGTTCGCGCACGGCACCTTCGAGCTCTGGC
TCCACCCGTCCCGCTACCGCACCCGCCCCTGCCGCGCCGGCCCGGCCTGCCGCCGCCGCGTCTGCTTCTTCGCGCACGCG
GCCGGGGAGCTCCGCCTCGCCTCCCACCACAAGGGGCCGGGGCCGGACTCGCCGCCGGCGCTGTCGCCCAAGTCCACGCT
GACGGCGCTCTGGGAGTCGCCCCCGGTGTCGCCCGTGGAGGGCAGGATGAGGTGGCTGGACGCCATAGACGACGCCGCCG
CCGCCGACGCCGAGGTCGGGGAGATCATGCTCGCAATGCAGCAGCTCAGCTTCGCCAACGCAGCA------------CCG
TCAGGAACGCTGCCGGCGGTGACGGAGGACGACGGGCCGGACCTGGGGTGGGTGTCGGAGCTGGTCATGTGATCAATCAG
GAGACGGAAGCCCCACCAA-------------------GCAGCAAGCAAGACAG-CAGCAGCTTCAGTAATTAATTAATT
ACTCGTATTATATTAAGCAACCTATTATTAAATTCTACCATTCCCGGAGTCGGATGCATCATTCTTCTGTAGATAAACAA
GCGCGTATGTATGGTGCAAGCTGAATACAGCAAAGAATTGTAAAATTATTAAGC-------------GTGAGTGCCTGTT
TTTTT-TTCGAGACCGTCAATGGTTTCGGATTAGTGGGAACTAAATGAGTGTAATGGGCT-AGTAGCCTGCCGCTGTTTC
GTGATCTATAATATCATTTGATTTGATGTACTT--CG-AGTGCAGCTAGCGGTGTCTCGAATCTGCGTGCCACTAATTGT
CTATGTGCTTGACTTTGTTGATC-AGTTAGATTCTGCGAGGATCGGCTATGGACTTGTGAGGATGGGTCTCTTTCCTATG
TGAGCTATCCGGCTCCTC--------CTTTCTCCTTTCGGTCAAGCACTCACGCTCAGTGAGTCCCAACTTC----AATT
CTTTGACTTCTTATAATCGCTCATGATATATACATTATTCGAGGCTACCTTTAACCACGGGTCAGCAGGGTTAGCACAAT
GACATGCAACATGCATGTTGCGGGAAATTTTCAAACGAACAATTTCAACAATTTCTTATTTTATTATGTTCAACTTTATG
TATTCCTCTATCCATATAGTACATTAAATGTATAGAAATGGCTATAACAGAGTTGATACATCCATGCATGTGACAAGTAA
TTCCAAACGTAAGGAGTATATCATACATCTTAAATACTAATAGTTTTATCATTGATTATATTCTACCTTAAATACGTATT
AGGTCCTATATATATATGAAAGGAGGGGTATGAAAATTCGGAGAAAAGCCACTTGTCCCAAAAGAGAAAAGCCACTTGTC
CCAAAAGAGAAGAGGGCACAACCCATTAGTTTGGTAGGGGGGTGGCTTGGCCCTCTGATGATATATATAATCATAGCTAG
TGA
>chr1B_244
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---AGAAGAGAAACAAAAATAAAGGCGGCCGGG----GTGCGTGCGTGCCGGCGGCCGAGGAG------------AGAAA
CCATCCCGGCCGCGACGTGGCGGGCAACATGCAGCACCCGCCTCGACGCCGCTCCACGTACCCTCGCCCACCCCCACGTA
CCCCGCCCCGCGCCAAAACCACCCCACGCCGATAGCCCCCTGCCCGCAACCAACAGCGGTCCATGCGATACCGCCCCTCC
T----------CGCGTCCCGCCCCCGCCGCGCCACCCGCCTGTATAAAGCGACGCGCCACCCGCCCCACGCCCT------
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----------------------------GCTCCCTCACACCACCACACCACTACCACCACCGCCGGTTACCGTCACGGCG
TGTCA---CACCTCCCTCTCT--CCCTCTCCCTCTCTGACAAGGGCA------GCCATGGCGAGCCACGTCCACGGGCAC
GGCCTGCTGCTCGACCCGGCCGCGCTGGCCTACTCCTGGGCCGCCGAGCCGGAGATCCCGCCGCAGCTGCTCGCCGCGCT
CGGGGAGTACCTCTCCAACTCCGCCGCCGCCGG------CTCCCACGGGGACAACCAGTCTGCCGTCGACACCGAGTCCG
ACGCGGAGGCGGACGACGAGTTCATGATGTACGAGTTCAAGGTGCGGCGGTGCGCGCGCGCGCGGAGCCACGACTGGACC
GCCTGCCCCTACGCGCACCCGGGGGAGGCCGCGCGGCGCCGGGACCCGCGCCGCGTCGCGTACGCGGGCGAGCCCTGCCC
GGACTTCCGCCGCCGCCCCGGCGCCGCGTGCCCGCGCGGGTCCTCCTGCCCGTTCGCGCACGGCACCTTCGAGCTCTGGC
TCCACCCGTCCCGCTACCGCACCCGCCCCTGCCGCGCCGGCCCGGCCTGCCGCCGCCGCGTCTGCTTCTTCGCGCACGCG
GCCGGGGAGCTCCGCCTCGCCTCCCACCACAAGGGGC------CGGACTCGCCGCTGGCGCTGTCGCCCAAGTCCACGCT
CACCGCGCTCTGGGAGTCGCCCCCGGTGTCGCCGGTGGAGGGCAGGATGAGGTGGCTGGACGGCATAGACGACGCT----
--GCCGACGCCGAGGTCGAGGAGATCATGCTCGCAATGCAGCAGCTCAGCTTCGCCAACGCAGCAGCACCGTCGGCACCG
TCCGGTACGCTGCCGGCGGTGACGGAGGACGACGGGCCGGACCTGGGGTGGGTGTCGGAGCTGGTCATGTGATCAATCAA
GACACCGAAGCCCCACCAGCAGCACTCCTCGTGCCCCGGCAGCAAGCAAGACGGACAGCAGCTTCAGTAATTAATTAATT
ACTCCTATTATAGTAAGCAACCTATTA----ATTCTACCATTCGCGGAACCGGATGCATCATTCTTCTGTAGATAAACAA
GCGCGTATG----GTGCAAGCTGAATACAGCAAAGAATTGTAAAACTATTAAGCGTGGCGTTCGTGTGTGAGTGCCTGTT
TTTTG-TCCGAGACCAGCAACGGTTTTGGATTACTTGGAACTAAATGGTTGTAATGGGCTTAGTAGCCTCCCCCTGTTTC
GTGATATATAATATCATTTGATTTGATGTACTACTTCAAGTGCAGCTAGCGGTGTCTCAAATCTGTGTGCCACTAATTAT
CTATGTGCTTGACTTTGTTGATT-AGTTAGATTCTGCAAGGATCGGCTCTTGACTTGTGAGGATGGGTCTCTTTCCTATG
TGAGCTATCTGGCATTCTGGCCCCTTCTTTTTCCTTTCGGTCAAGCACTCACGCTCAGTCAGTC----------------
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>chr1D_270
CGGGG---------------------------------------------------------------------------
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--------------------------------------TGCGTGCGTGCCGGCGGCCGAGGAGGCTTGCGCGGGGAGAAA
CCATCCCGGCCGCGACGTGGCGGGCAACATGCAGCACCCGCCTCGACGGCGCTCCACGTACCCTCGCCCACCCCCACGTA
CCCCGCCCCGCGCCAAAACCACCCCACGCCGATAG-CCCCCGCCCGCAACCAACAGCGGTCCATGCGATACCGCCCCTCC
CCGCAGCGGCGCGCGTCCCGCCCCCGCCG------------GTATAAAGCGACGCGCCACCCGCCCCACGCCCT------
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----------------------------GCTCCCCCACACCACCA--CCGCCGCCGCCGCCGCCGGTTACCGTCACGGCG
TGTCA---CACCCCTCTCTCTTTCCCTCTCCCCCTCTGACAAGGACA------GCCATGGCGAGCCACGCGCACGGGCAC
GGCCTGCTGCTCGACCCGGCCGCGCTCGCCTACTCCTGGGCCGCCGAGCCGGAGATCCCGCCGCAGCTGCTCGCCGCGCT
GGGCGAGTACCTCTCCTCCTCCGCCGCT---GG------CTCCCACGGGGGCAACCAGTCTGCCGTCGACGCCGAGGCCG
ACGCGGAGGCGGACGACGAGTTCATGATGTACGAGTTCAAGGTGCGGCGGTGCGCGCGCGCGCGGAGCCACGACTGGACG
GCCTGCGCCTACGCGCACCCGGGGGAGGCGGCGCGGCGCCGGGACCCGCGCCGCGTGGCCTACGCGGGGGAGCCATGCCC
GGACTTCCGCCGCCGCCCGGGCGCCGCGTGCCCGCGCGGGGCCTCCTGCCCCTTCGCGCACGGCACCTTCGAGCTCTGGC
TCCACCCGTCCCGCTACCGCACCCGCCCCTGCCGCGCCGGCCCGGCCTGCCGCCGCCGCGTCTGCTTCTTCGCGCACGCG
GCCGGGGAGCTCCGCCTCGCCTCCCACCACAAGGGGC------CCGACTCGCCGCTGGCGCTGTCGCCCAAGTCCACGCT
CACCGCGCTCTGGGAGTCGCCCCCGGTGTCGCCGGTGGAGGGCAGGATGAGGTGGCTGGACGCCGTAGACGACGCCGCCG
CCGCCGACGCCGAGGTCGAGGAGATCATGCTCGCAATGCAGCAGCTCAGCTTCGCCAACGCAGCAGCACCGTCGGCACCG
TCGGGAACGCTGCCGGCGGTGACGGAGGACGACGGGCCGGACCTGGGGTGGGTGTCGGAGCTGGTCATGTGATCAATCAG
GAGACCGAAGCTCT-CCAGCAGCGCTCCTCGTGCCCCGGCAGCAAGCAAGACAG-CAGCAGCTCCAGTAATTAATTAAGT
ACTCCTATTATATTAAGCAACCTATTA----AATTCTACC-------------ATGCATCATTCTTCTGTAGATAAACAA
GCGCGTATG----GTGCAAGCTGAATACAGCAAAGAATTGTAAAATTGTTAAGCGTGGCGTTCGTGTGTGAGCGCCTGTT
TTTTTTTCCGAGACCAGCAATGGTTTTGGATTAGTTGGAACTAAATGAGTGTAATGGGCT-AGTAGCCTCCCCTTGTTTC
GTGATCTATAATATCATTTGATTTGATGGTACTTCCG-AGTGCAGCTAGCGGTGTCTCGAATCTGTGTGCCACTAATAAT
CCATGTGCTTGACTTTGTTCATTAAGTTAGATTCTGCAAGGATCGGCTCTGGACTTCTGAGGATGGGTCTCTTTCCTATG
TGAGCTATCCGGCTCCTC--------CTTTTTCCTTTCGGTCAAGCACTCACGCTCAGTGAGTCTCAGCTTGCTTGAATT
CTTTGACTTTCTATATA---------------------------------------------------------------
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>SNPs
-S-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS-------S--S--------------S----SSSS-------------------S-----------------------
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-----S------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSS----------------------------------------------------
-----SSS-----------S---------------------------SSSSSS----------------S---S-S----
------------------------------------------------------S-------------------------
--------------------------------SSSSSSS-------------S-S--------------S-----S--S-
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------------------------------------S-------------------------------------------
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-------------------------------------SSSSSS------------S------------------------
S--S-----------------------------S----------------------------------------------
------------------S-------------------------------------------------------------
--S-----------------------------------------------------------------------------
-----S------------S-------------------------------------------------------------
----S----------------------SSSS------------S----SS------------------------------
---------SSSS-------------------------------------------------------------------
-------S-------SS---------S--------S---------------------------------S--S-------
-----------------------------------------------------------------S------------S-
----------------------S--------------S----------S-------------------------------
------------------------------S---------------------------------S--S---S--------
---------SS----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSS
>forward_1008
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----------------------------TCCCCCTCTGACAAGGACAA--------------------------------
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>reverse_2448
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-----------------------------------------------CCTTTAACCACGGGTCAGCA-------------
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